Update template to v0.3.1

.cruft.json

@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
-  "checkout": "v0.3.0",
+  "commit": "586b1652162ff7994b0070a034023d64289ae416",
+  "checkout": "v0.3.1",
   "context": {
     "cookiecutter": {
       "project_name": "biolord",
@@ -13,7 +13,8 @@
       "project_repo": "https://github.com/nitzanlab/biolord",
       "license": "BSD 3-Clause License",
       "_copy_without_render": [
-        ".github/workflows/**.yaml",
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
         "docs/_templates/autosummary/**.rst"
       ],
       "_render_devdocs": false,

.github/workflows/release.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/{{ cookiecutter.package_name }}
+      url: https://pypi.org/p/biolord
     permissions:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:

.pre-commit-config.yaml.rej

@@ -1,100 +1,34 @@
 diff a/.pre-commit-config.yaml b/.pre-commit-config.yaml	(rejected hunks)
-@@ -1,50 +1,53 @@
- fail_fast: false
- default_language_version:
--    python: python3
-+  python: python3
- default_stages:
--    - commit
--    - push
-+  - commit
-+  - push
+@@ -6,29 +6,18 @@ default_stages:
+   - push
  minimum_pre_commit_version: 2.16.0
  repos:
--    - repo: https://github.com/psf/black
--      rev: "23.11.0"
--      hooks:
--          - id: black
--    - repo: https://github.com/asottile/blacken-docs
--      rev: 1.16.0
--      hooks:
--          - id: blacken-docs
--    - repo: https://github.com/pre-commit/mirrors-prettier
--      rev: v3.1.0
--      hooks:
--          - id: prettier
--            # Newer versions of node don't work on systems that have an older version of GLIBC
--            # (in particular Ubuntu 18.04 and Centos 7)
--            # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
--            # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
--            # https://github.com/jupyterlab/jupyterlab/issues/12675
--            language_version: "17.9.1"
--    - repo: https://github.com/charliermarsh/ruff-pre-commit
--      rev: v0.1.6
--      hooks:
--          - id: ruff
--            args: [--fix, --exit-non-zero-on-fix]
--    - repo: https://github.com/pre-commit/pre-commit-hooks
--      rev: v4.5.0
--      hooks:
--          - id: detect-private-key
--          - id: check-ast
--          - id: end-of-file-fixer
--          - id: mixed-line-ending
--            args: [--fix=lf]
--          - id: trailing-whitespace
--          - id: check-case-conflict
--    - repo: local
--      hooks:
--          - id: forbid-to-commit
--            name: Don't commit rej files
--            entry: |
--                Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
--                Fix the merge conflicts manually and remove the .rej files.
--            language: fail
--            files: '.*\.rej$'
-+  - repo: https://github.com/psf/black
-+    rev: "23.11.0"
-+    hooks:
-+      - id: black
-+  - repo: https://github.com/asottile/blacken-docs
-+    rev: 1.16.0
-+    hooks:
-+      - id: blacken-docs
-+  - repo: https://github.com/pre-commit/mirrors-prettier
-+    rev: v3.1.0
-+    hooks:
-+      - id: prettier
-+        # Newer versions of node don't work on systems that have an older version of GLIBC
-+        # (in particular Ubuntu 18.04 and Centos 7)
-+        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
-+        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
-+        # https://github.com/jupyterlab/jupyterlab/issues/12675
-+        language_version: "17.9.1"
-+  - repo: https://github.com/astral-sh/ruff-pre-commit
-+    rev: v0.1.6
-+    hooks:
-+      - id: ruff
-+        args: [--fix, --exit-non-zero-on-fix]
-+  - repo: https://github.com/pre-commit/pre-commit-hooks
-+    rev: v4.5.0
-+    hooks:
-+      - id: detect-private-key
-+      - id: check-ast
-+      - id: end-of-file-fixer
-+      - id: mixed-line-ending
-+        args: [--fix=lf]
-+      - id: trailing-whitespace
-+      - id: check-case-conflict
-+      # Check that there are no merge conflicts (could be generated by template sync)
-+      - id: check-merge-conflict
-+        args: [--assume-in-merge]
-+  - repo: local
-+    hooks:
-+      - id: forbid-to-commit
-+        name: Don't commit rej files
-+        entry: |
-+          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
-+          Fix the merge conflicts manually and remove the .rej files.
-+        language: fail
-+        files: '.*\.rej$'
+-  - repo: https://github.com/psf/black
+-    rev: "24.2.0"
+-    hooks:
+-      - id: black
+-  - repo: https://github.com/asottile/blacken-docs
+-    rev: 1.16.0
+-    hooks:
+-      - id: blacken-docs
+   - repo: https://github.com/pre-commit/mirrors-prettier
+     rev: v4.0.0-alpha.8
+     hooks:
+       - id: prettier
+-        # Newer versions of node don't work on systems that have an older version of GLIBC
+-        # (in particular Ubuntu 18.04 and Centos 7)
+-        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+-        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+-        # https://github.com/jupyterlab/jupyterlab/issues/12675
+-        language_version: "17.9.1"
+   - repo: https://github.com/astral-sh/ruff-pre-commit
+     rev: v0.2.2
+     hooks:
+       - id: ruff
++        types_or: [python, pyi, jupyter]
+         args: [--fix, --exit-non-zero-on-fix]
++      - id: ruff-format
++        types_or: [python, pyi, jupyter]
+   - repo: https://github.com/pre-commit/pre-commit-hooks
+     rev: v4.5.0
+     hooks:

pyproject.toml

@@ -62,12 +62,15 @@ addopts = [
     "--import-mode=importlib",  # allow using test files with same name
 ]
 
-[tool.black]
-line-length = 120
-
 [tool.ruff]
-src = ["src"]
 line-length = 120
+src = ["src"]
+extend-include = ["*.ipynb"]
+
+[tool.ruff.format]
+docstring-code-format = true
+
+[tool.ruff.lint]
 select = [
     "F",  # Errors detected by Pyflakes
     "E",  # Error detected by Pycodestyle
@@ -82,7 +85,7 @@ select = [
     "RUF100",  # Report unused noqa directives
 ]
 ignore = [
-    # line too long -> we accept long comment lines; black gets rid of long code lines
+    # line too long -> we accept long comment lines; formatter gets rid of long code lines
     "E501",
     # Do not assign a lambda expression, use a def -> lambda expression assignments are convenient
     "E731",

pyproject.toml.rej

@@ -1,40 +1,37 @@
 diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
-@@ -7,7 +7,7 @@ name = "biolord"
- version = "0.0.1"
- description = "A deep generative framework for disentangling known and unknown attributes in single-cell data."
- readme = "README.md"
--requires-python = ">=3.8"
-+requires-python = ">=3.9"
- license = {file = "LICENSE"}
- authors = [
-     {name = "Zoe Piran"},
-@@ -26,25 +26,26 @@ dependencies = [
+@@ -21,13 +21,13 @@ urls.Home-page = "https://github.com/nitzanlab/biolord"
+ dependencies = [
+     "anndata",
+     # for debug logging (referenced from the issue template)
+-    "session-info"
++    "session-info",
+ ]
 
  [project.optional-dependencies]
  dev = [
--    # CLI for bumping the version number
--    "bump2version",
      "pre-commit",
-     "twine>=4.0.2"
+-    "twine>=4.0.2"
++    "twine>=4.0.2",
  ]
  doc = [
-+    "docutils>=0.8,!=0.18.*,!=0.19.*",
-     "sphinx>=4",
-     "sphinx-book-theme>=1.0.0",
-     "myst-nb",
-     "sphinxcontrib-bibtex>=1.0.0",
-     "sphinx-autodoc-typehints",
-+    "sphinxext-opengraph",
-     # For notebooks
-     "ipykernel",
-     "ipython",
-     "sphinx-copybutton",
-+    "pandas",
- ]
- test = [
-     "pytest",
--    "pytest-cov",
-+    "coverage",
+     "docutils>=0.8,!=0.18.*,!=0.19.*",
+@@ -108,10 +111,10 @@ ignore = [
+     "D213",
  ]
 
- [tool.coverage.run]
+-[tool.ruff.pydocstyle]
++[tool.ruff.lint.pydocstyle]
+ convention = "numpy"
+
+-[tool.ruff.per-file-ignores]
++[tool.ruff.lint.per-file-ignores]
+ "docs/*" = ["I"]
+ "tests/*" = ["D"]
+ "*/__init__.py" = ["F401"]
+@@ -125,5 +128,5 @@ skip = [
+     "docs/changelog.md",
+     "docs/references.bib",
+     "docs/references.md",
+-    "docs/notebooks/example.ipynb"
++    "docs/notebooks/example.ipynb",
+ ]